Transcript Association Study of Age of Diagnosis of Type 1 Diabetes using

FSTL4 and SEMA5A are associated
with alcohol dependence: metaanalysis of two genome-wide
association studies
Kesheng Wang, PhD
Department of Biostatistics and Epidemiology
College of Public Health
East Tennessee State University
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Outline
• Introduction
 Alcohol dependence (AD)
 Genetic study
• Subjects and Methods
 Design, genotyping and statistics
• Results
• Conclusions
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What is Alcohol Dependence (AD)?
• Alcoholism, also known as alcohol dependence
(AD), is a disease that includes the following four
symptoms:
• Craving--A strong need, or urge, to drink.
• Loss of control--Not being able to stop drinking
once drinking has begun.
• Physical dependence--Withdrawal symptoms,
such as nausea, sweating, shakiness, and
anxiety after stopping drinking.
• Tolerance--The need to drink greater amounts
of alcohol to get "high."
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Is There a Genetic Influence of AD?
• Family, twin, and adoption studies have
demonstrated that genes play a major role in the
development of alcohol dependence (Heath,
1995).
• Heritability estimates range from 50% to 60% for
both men and women (Prescott et al., 1999).
In genetics, Heritability is the proportion of
phenotypic variation in a population that is
attributable to genetic variation among individuals.
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Genome-wide Association Studies (GWAS)
and International HapMap Project
• The prospect of GWAS was firstly proposed in
1996 (Risch & Merikangas, Science 1996)
• GWAS will involve screening a subset of
common genetic variation in human genome on
large samples (300K-500K genetic markers)
• The advances of human genome project
(sequence project completed in 2000) and
especially International HapMap Project (in
2005, 2007 and 2009) made these studies
possible.
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PHASE I – more than 1M common SNPs were
typed (inter-marker spacing 5kb) (2005)
PHASE II – more than 3M common SNPs were
typed (2007)
PHASE III – data released (2009)
Totally, about 6,000,000 common SNPs
(Minor Allele Frequency >5%) in human
genome
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What is a SNP?
A single-nucleotide polymorphism
(SNP) is a DNA sequence variation
occurring when a single nucleotide — A,
T, C, or G — in the genome differs
between members of a species.
e.g., Two DNA fragments from 2
individuals, AAGCCTA to AAGCTTA,
contain a difference in a single
nucleotide.
We say there are two alleles : C & T.
One SNP has two alleles (e.g., A and a
or 1 and 2) and 3 genotypes (AA, Aa
and aa or 11, 12 and 22)
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Genome-Wide Association Studies in AD
• Recently, several GWAS in AD have been
conducted to identify common genetic
variants which affect risk of AD
• 1. German male sample (Treutlein et al.,
2009).
• 2. SAGE sample (Bierut et al. 2010)
• 3. COGA sample (Edenberg et al. 2010)
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Motivation of This Study
• The GWAS is a powerful tool for unlocking the
genetic basis of complex diseases such as AD.
• Hypothesis – free (search the entire genome for
associations rather than candidate areas).
• A powerful tool to identify disease-related genes
for many complex human disorders
• However, few genetic loci were replicated in
different studies. No meta-analysis of GWAS.
• Objective: To conduct meta-analysis of
two genome-wide association datasets to
search for novel genetic variants
associated with risk of AD
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Subjects and Methods
• COGA data includes 734 AD patients and 440
controls. 1M SNPs
• For AD, we define 2 as affected, 1 as
unaffected.
• SAGE data includes 637 AD patients and 1033
controls. 1M SNPs
• Australian Twin-Family Study of Alcohol Use
Disorder dataset with 778 families. 370K SNPs
• Each SNP has two alleles (1 and 2). Genotypes
for each SNP were coded as 1/1, 1/2 and 2/2
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The Principle of Association for Binary Trait (AD)
• In a population, for one SNP: 3 type
genotypes, AA, Aa and aa.
• Chi-square test based on 2 x 3 table
• Simple logistic model
• Yi      X i   i
• Multiple logistic model
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PLINK software – GWAS analysis
• Logistic model in PLINK - Odds ratio (OR) and SE
(Standard error of OR) and P-values.
• Meta-analysis: Fixed-effects meta-regression
model in PLINK
• P - Fixed-effects meta-analysis p-value
• OR - Fixed-effects odds ratio (OR)
• Q - p-value for Cochrane's Q statistic
 Q statistics is a method widely utilized to test the
assumption that all studies share a common
population effect size is the homogeneity test.
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Results of AD
• We identified 81 SNPs associated with AD (p <
10-4)
• Top 3 genes associated wit AD
 rs930076 (p=3.86x10-6, Q=0.72) at 5p15.2 within
SEMA5A gene
 rs155581 (p=7.63x10-6, Q=0.97) at 5q31.1 within
FSTL4
 PKNOX2 at 11q24.3 with alcohol dependence
(the top SNP is rs1426153 with p = 8.36x10-6,
Q=0.61).
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Replication Study
• Top SNPs for three genes in Twin family
study
• rs950050 with p= 0.014, SEMA5A
• rs407758 with p=0.0066, FSTL4
• rs2509449 with p=0.0023, PKNOX2
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Conclusions and Discussion
• Identified 3 loci using meta-analysis
• Replicated associations in additional
family-based association study
• SEMA5A is previously associated with
Parkinson disease and autism
• FSTL4 is previously associated with
stroke and linked to schizophrenia.
• PNOKX2 is previously associated with
AD.
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Importance of Genetic Effects for
Clinical Practice
• Increasingly medical interventions target
specific genes
– Differential treatment effects
– More effective medications, less severe side effect
profile
• Prevention and early detection
– Early screening and population screening
• Gene and environment interplay
- gender difference
- race difference
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Take Home Messages
• AD is genetically controlled
• Genetic findings open valuable possibilities for the
future of medicine
– Greater understanding of biologic pathways
– Prediction of the risk
– Prevention of the diseases
– Development of new treatment
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Acknowledgement
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Dr. Xuefeng Liu (Department of Biostatistics
and Epidemiology)
Dr. Qunyuan Zhang (Washington University
School of Medicine, St. Louis)
Yue Pan (Ms Student)
Nagesh Aragam (DrPH student)
Min Zeng (Visiting scholar)
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Kesheng Wang